How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications

Konermann, Lars; Metwally, Haidy; McAllister, Robert G.; Popa, Vlad Tudor

doi:10.1016/j.ymeth.2018.04.010

Cited by 46 publications

(77 citation statements)

References 100 publications

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“…These approaches, along with examples from the literature, are summarized in Table 1. A recent review by Konermann discusses other MD simulation parameters and their impact on results [51]. With simulated structures in hand, ion CCSs in the relevant IM-MS buffer gas can be predicted using a variety of computational tools with tradeoffs in physical realism and computational expense.…”

Section: What Happens To Folded Protein Ions Upon Transfer To the Gasmentioning

confidence: 99%

“…During the last decade or so, efforts to accurately simulate desiccation of biomolecules within ESI droplets and concomitant acquisition of charge have been undertaken by several groups [36,37,44,45,51,67,[74][75][76][77]. In addition to the aforementioned simulations by Steinberg et al [48], the Konermann and Consta groups have applied MD simulations to charged droplets containing biomolecules to learn about ionization mechanisms, ion compaction upon desiccation, and heating-induced unfolding and dissociation.…”

Section: Explicit Modeling Of Nesi Droplet Evaporation and Ion Chargimentioning

confidence: 99%

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Computational insights into compaction of gas-phase protein and protein complex ions in native ion mobility-mass spectrometry

Rolland

Prell

2019

TrAC Trends in Analytical Chemistry

103

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Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.

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Section: What Happens To Folded Protein Ions Upon Transfer To the Gasmentioning

confidence: 99%

Section: Explicit Modeling Of Nesi Droplet Evaporation and Ion Chargimentioning

confidence: 99%

Computational insights into compaction of gas-phase protein and protein complex ions in native ion mobility-mass spectrometry

Rolland

Prell

2019

TrAC Trends in Analytical Chemistry

103

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“…Electrospray ionization (ESI) is the primary ionization technique for ionizing polar organic compounds. In an optimized ESI condition, ions are generated from the dissociation of a charged droplet, leaving a stream of ions . Using collision‐induced dissociation (CID), the ions, which entered the mass spectrometer can collide with an inert gas, typically nitrogen, to obtain product ion spectra, and is commonly combined with ESI (ESI‐CID or ESI‐MS/MS).…”

Section: Introductionmentioning

confidence: 99%

“…In an optimized ESI condition, ions are generated from the dissociation of a charged droplet, leaving a stream of ions. 20 Using collision-induced dissociation (CID), the ions, which entered the mass spectrometer can collide with an inert gas, typically nitrogen, to obtain product ion spectra, and is commonly combined with ESI (ESI-CID or ESI-MS/MS). Atmospheric pressure chemical ionization (APCI) is an alternative to ESI, which produces a corona discharge whereby atmospheric gases, such as O 2 and N 2 , are ionized and further react with analyte molecules.…”

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confidence: 99%

Comparison of ESI‐MS/MS and APCI‐MS methods for the quantification of folic acid analogs in C. elegans

et al. 2019

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Folic acid (FA) plays a vital role in central metabolism, including the one carbon cycle, nucleotide, and amino acid biosynthesis. The development of sensitive, accurate analytical methods to measure FA intermediates in tissues is critical to understand their biological roles in diverse physiological and pathological contexts. Here, we developed a highly sensitive method for the simultaneous quantification of FA intermediates in the nematode Caenorhabditis elegans as a model to dissect metabolic networks. The method was further validated by analyzing the worm folate pool upon RNAi knockdown of the dihydrofolate reductase gene dhfr‐1. Comparative mass spectrometry behavior of the FA analogs using two different ion sources, electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), revealed ESI‐MS/MS to be more sensitive, but APCI‐MS provided more detailed structure inferences, which can elucidate chemical investigation and synthesis of FA analogs. Finally, we report on the use of in vitro oxidation coupled with high‐resolution mass spectrometry as a tool to discover new endogenous FA derivatives in the nematode.

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“…Novel research is emerging using MD simulations to provide insights into the behavior of molecules in the experiments. For some reviews, see [ 93 , 96 ].…”

Section: Mass Spectrometrymentioning

confidence: 99%

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

2020

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Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.

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How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications

Cited by 46 publications

References 100 publications

Computational insights into compaction of gas-phase protein and protein complex ions in native ion mobility-mass spectrometry

Computational insights into compaction of gas-phase protein and protein complex ions in native ion mobility-mass spectrometry

Comparison of ESI‐MS/MS and APCI‐MS methods for the quantification of folic acid analogs in C. elegans

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

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